Publications

2014

Cortes-Ciriano, Isidro, Gerard J. P. van Westen, Eelke Bart Lenselink, Daniel S. Murrell, Andreas Bender, and Thérèse Malliavin.
"Proteochemometric Modeling in a Bayesian Framework." J Cheminform 6, no. 1 (2014): 35.
DOI: 10.1186/1758-2946-6-35

Costello, J. C., L. M. Heiser, E. Georgii, M. Gonen, M. P. Menden, N. J. Wang, M. Bansal, M. Ammad-Ud-Din, P. Hintsanen, S. A. Khan, J. P.
Mpindi, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg, J. J. Collins, D. Gallahan, D. Singer, J. Saez-Rodriguez, S. Kaski, J. W.
Gray, and G. Stolovitzky. "A Community Effort to Assess and Improve Drug Sensitivity Prediction Algorithms." Nat Biotechnol, (2014).
DOI: 10.1038/nbt.2877

Dizdarevic, S., R. McCready, J. F. Turner, M. C. Bagley, P. Blower, P. Schmid, G. Flux, A. Hall, and I. Ziv. "Radiolabelled Apoptotic Probe
May Be a Vehicle for a Novel Multimodality Radionuclide Tumour Therapy." Eur J Nucl Med Mol Imaging 41, no. 6 (2014): 1255-6.
DOI: 10.1007/s00259-014-2725-7

Oliveri, V., F. Attanasio, A. Puglisi, J. Spencer, C. Sgarlata, and G. Vecchio. "Multifunctional 8-Hydroxyquinoline-Appended Cyclodextrins
as New Inhibitors of Metal-Induced Protein Aggregation." Chemistry, (2014).
DOI: 10.1002/chem.201402690

van Westen, G. J., A. Gaulton, and J. P. Overington. "Chemical, Target, and Bioactive Properties of Allosteric Modulation." PLoS Comput Biol
10, no. 4 (2014): e1003559.
DOI: 10.1371/journal.pcbi.1003559

van Westen, Gerard J. P., Andreas Bender, and John P. Overington. "Towards Predictive Resistance Models for Agrochemicals by Combining
Chemical and Protein Similarity Via Proteochemometric Modelling." Journal of Chemical Biology, (2014).
DOI: 10.1007/s12154-014-0112-2

Bento, A. P., A. Gaulton, A. Hersey, L. J. Bellis, J. Chambers, M. Davies, F. A. Kruger, Y. Light, L. Mak, S. McGlinchey, M. Nowotka, G. 
Papadatos, R. Santos, and J. P. Overington. "The Chembl Bioactivity Database: An Update." Nucleic Acids Res 42, no. Database issue (2014): 
D1083-90. DOI: 10.1093/nar/gkt1031

 

2013 

Burrows, A. D., M. Jurcic, L. L. Keenan, R. A. Lane, M. F. Mahon, M. R. Warren, H. Nowell, M. Paradowski, and J. Spencer. "Incorporation by Coordination and Release of the Iron Chelator Drug Deferiprone from Zinc-Based Metal-Organic Frameworks." Chem Commun (Camb) 49, no. 96 (2013): 11260-2. DOI: 10.1039/c3cc45689g

De Bruyn, T., G. J. van Westen, A. P. Ijzerman, B. Stieger, P. de Witte, P. F. Augustijns, and P. P. Annaert. "Structure-
Based Identification of Oatp1b1/3 Inhibitors." Mol Pharmacol 83, no. 6 (2013): 1257-67. DOI:10.1124/mol.112.084152

Deuss, P. J., A. A. Arzumanov, D. L. Williams, and M. J. Gait. "Parallel Synthesis and Splicing Redirection Activity of
Cell-Penetrating Peptide Conjugate Libraries of a Pna Cargo." Org Biomol Chem 11, no. 43 (2013): 7621-30.
DOI:10.1039/C3OB41659C

Edwards, J. M., J. Long, C. H. de Moor, J. Emsley, and M. S. Searle. "Structural Insights into the Targeting of Mrna Gu-
Rich Elements by the Three Rrms of Celf1." Nucleic Acids Res 41, no. 14 (2013): 7153-66. DOI: 10.1093/nar/gkt470

Foot, J. N., M. Feracci, and C. Dominguez. "Screening Protein - Single Stranded Rna Complexes by Nmr Spectroscopy for
Structure Determination." Methods, (2013). DOI: 10.1016/j.ymeth.2013.09.018 

Gammons, M. V., O. Fedorov, D. Ivison, C. Du, T. Clark, C. Hopkins, M. Hagiwara, A. D. Dick, R. Cox, S. J. Harper, J. C.
Hancox, S. Knapp, and D. O. Bates. "Topical Antiangiogenic Srpk1 Inhibitors Reduce Choroidal Neovascularization in Rodent
Models of Exudative Amd." Invest Ophthalmol Vis Sci 54, no. 9 (2013): 6052-62. DOI: 10.1167/iovs.13-12422

Kenyon, J. C., L. J. Prestwood, S. F. Le Grice, and A. M. Lever. "In-Gel Probing of Individual Rna Conformers within a
Mixed Population Reveals a Dimerization Structural Switch in the Hiv-1 Leader." Nucleic Acids Res 41, no. 18 (2013): e174.
DOI: 10.1093/nar/gkt690 

Knapp, S., P. Arruda, J. Blagg, S. Burley, D. H. Drewry, A. Edwards, D. Fabbro, P. Gillespie, N. S. Gray, B. Kuster, K. E.
Lackey, P. Mazzafera, N. C. Tomkinson, T. M. Willson, P. Workman, and W. J. Zuercher. "A Public-Private Partnership to
Unlock the Untargeted Kinome." Nat Chem Biol 9, no. 1 (2013): 3-6. DOI: 10.1038/nchembio.1113

Liu, X., R. Wilcken, A. C. Joerger, I. S. Chuckowree, J. Amin, J. Spencer, and A. R. Fersht. "Small Molecule Induced
Reactivation of Mutant P53 in Cancer Cells." Nucleic Acids Res 41, no. 12 (2013): 6034-44. DOI: 10.1093/nar/gkt305

Oliveri, V., A. Puglisi, M. Viale, C. Aiello, C. Sgarlata, G. Vecchio, J. Clarke, J. Milton, and J. Spencer. "New
Cyclodextrin-Bearing 8-Hydroxyquinoline Ligands as Multifunctional Molecules." Chemistry 19, no. 41 (2013): 13946-55. DOI:
10.1002/chem.201300237 

Talapatra, S. K., N. G. Anthony, S. P. Mackay, and F. Kozielski. "Mitotic Kinesin Eg5 Overcomes Inhibition to the Phase
I/Ii Clinical Candidate Sb743921 by an Allosteric Resistance Mechanism." J Med Chem 56, no. 16 (2013): 6317-29. DOI: 10.1021/jm4006274 

Trump, R. P., S. Bresciani, A. W. Cooper, J. P. Tellam, J. Wojno, J. Blaikley, L. A. Orband-Miller, J. A. Kashatus, M.
Boudjelal, H. C. Dawson, A. Loudon, D. Ray, D. Grant, S. N. Farrow, T. M. Willson, and N. C. Tomkinson. "Optimized
Chemical Probes for Rev-Erbalpha." J Med Chem 56, no. 11 (2013): 4729-37. DOI:10.1021/jm400458q 

van Westen, G. J., A. Hendriks, J. K. Wegner, A. P. Ijzerman, H. W. van Vlijmen, and A. Bender. "Significantly Improved
Hiv Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated from Antivirogram Data." PLoS Comput Biol
9, no. 2 (2013): e1002899. DOI: 10.1371/journal.pcbi.1002899 

van Westen, G. J., and J. P. Overington. "A Ligand's-Eye View of Protein Similarity." Nat Methods 10, no. 2 (2013): 116-7.
DOI: 10.1038/nmeth.2339 

van Westen, G. J., R. F. Swier, I. Cortes-Ciriano, J. K. Wegner, J. P. Overington, A. P. Ijzerman, H. W. van Vlijmen, and
A. Bender. "Benchmarking of Protein Descriptor Sets in Proteochemometric Modeling (Part 2): Modeling Performance of 13
Amino Acid Descriptor Sets." J Cheminform 5, no. 1 (2013): 42. DOI: 10.1186/1758-2946-5-42 

van Westen, G. J., R. F. Swier, J. K. Wegner, A. P. Ijzerman, H. W. van Vlijmen, and A. Bender. "Benchmarking of Protein
Descriptor Sets in Proteochemometric Modeling (Part 1): Comparative Study of 13 Amino Acid Descriptor Sets." J Cheminform
5, no. 1 (2013): 41. DOI: 10.1186/1758-2946-5-41 

Wiejak, J., J. Dunlop, S. P. Mackay, and S. J. Yarwood. "Flavanoids Induce Expression of the Suppressor of Cytokine
Signalling 3 (Socs3) Gene and Suppress Il-6-Activated Signal Transducer and Activator of Transcription 3 (Stat3)
Activation in Vascular Endothelial Cells." Biochem J 454, no. 2 (2013): 283-93. DOI: 10.1042/BJ20130481

 

2012

Adams, C. J., A. C. Pike, S. Maniam, T. D. Sharpe, A. S. Coutts, S. Knapp, N. B. La Thangue, and A. N. Bullock. "The P53
Cofactor Strap Exhibits an Unexpected Tpr Motif and Oligonucleotide-Binding (Ob)-Fold Structure." Proc Natl Acad Sci U S A
109, no. 10 (2012): 3778-83. DOI: 10.1073/pnas.1113731109 

Alniss, Hasan Y., Nahoum G. Anthony, Abedawn I. Khalaf, Simon P. Mackay, Colin J. Suckling, Roger D. Waigh, Nial J.
Wheate, and John A. Parkinson. "Rationalising Sequence Selection by Ligand Assemblies in the DNA Minor Groove: The Case
for Thiazotropsin A." Chemical Science 3, no. 3 (2012): 711. DOI: 10.1039/C2SC00630H 

Chapman, M. A., S. Tang, D. Draeger, S. Nambeesan, H. Shaffer, J. G. Barb, S. J. Knapp, and J. M. Burke. "Genetic Analysis
of Floral Symmetry in Van Gogh's Sunflowers Reveals Independent Recruitment of Cycloidea Genes in the Asteraceae." PLoS
Genet 8, no. 3 (2012): e1002628. DOI: 10.1371/journal.pgen.1002628 

Clark, R. L., C. J. Clements, M. P. Barrett, S. P. Mackay, R. P. Rathnam, G. Owusu-Dapaah, J. Spencer, and J. K. Huggan.
"Identification and Development of the 1,4-Benzodiazepin-2-One and Quinazoline-2,4-Dione Scaffolds as Submicromolar
Inhibitors of Hat." Bioorg Med Chem 20, no. 20 (2012): 6019-33. DOI: 10.1016/j.bmc.2012.08.049 

Elkins, J. M., S. Santaguida, A. Musacchio, and S. Knapp. "Crystal Structure of Human Aurora B in Complex with Incenp and
Vx-680." J Med Chem 55, no. 17 (2012): 7841-8. DOI: 10.1021/jm3008954 

Eswaran, J., S. Gupta, A. Dutt, M. Toi, M. R. Pillai, L. Costa, S. Knapp, R. Badwe, R. Kumar, and Global Canc Genomics
Consortium. "The Global Cancer Genomics Consortium: Interfacing Genomics and Cancer Medicine." Cancer Research 72, no. 15
(2012): 3720-3724. DOI: 10.1158/0008-5472.Can-12-1054 

Filippakopoulos, P., S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S.
Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, and S. Knapp. "Histone Recognition and Large-Scale Structural Analysis
of the Human Bromodomain Family." Cell 149, no. 1 (2012): 214-31. DOI: 10.1016/j.cell.2012.02.013 

Gaulton, A., L. J. Bellis, A. P. Bento, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, D. Michalovich, B.
Al-Lazikani, and J. P. Overington. "Chembl: A Large-Scale Bioactivity Database for Drug Discovery." Nucleic Acids Res 40,
no. Database issue (2012): D1100-7. DOI: 10.1093/nar/gkr777 

Kruger, F. A., and J. P. Overington. "Global Analysis of Small Molecule Binding to Related Protein Targets." PLoS Comput
Biol 8, no. 1 (2012): e1002333. DOI: 10.1371/journal.pcbi.1002333 

Lane, J. R., C. Klein Herenbrink, G. J. van Westen, J. A. Spoorendonk, C. Hoffmann, and I. Jzerman AP. "A Novel Nonribose
Agonist, Luf5834, Engages Residues That Are Distinct from Those of Adenosine-Like Ligands to Activate the Adenosine a(2a)
Receptor." Mol Pharmacol 81, no. 3 (2012): 475-87. DOI: 10.1124/mol.111.075937 

Pasquo, A., V. Consalvi, S. Knapp, I. Alfano, M. Ardini, S. Stefanini, and R. Chiaraluce. "Structural Stability of Human
Protein Tyrosine Phosphatase Rho Catalytic Domain: Effect of Point Mutations." PLoS One 7, no. 2 (2012): e32555. DOI:
10.1371/journal.pone.0032555 

Petch, D., R. J. Anderson, A. Cunningham, S. E. George, D. E. Hibbs, R. Liu, S. P. Mackay, A. Paul, D. A. Small, and P. W.
Groundwater. "Design and Synthesis of Egfr Dimerization Inhibitors and Evaluation of Their Potential in the Treatment of
Psoriasis." Bioorg Med Chem 20, no. 19 (2012): 5901-14. DOI: 10.1016/j.bmc.2012.07.048 

Spencer, John, Jahangir Amin, Ramesh Boddiboyena, Graham Packham, Breeze E. Cavell, Sharifah S. Syed Alwi, Ronald M.
Paranal, Tom D. Heightman, Minghua Wang, Brian Marsden, Peter Coxhead, Matthew Guille, Graham J. Tizzard, Simon J. Coles,
and James E. Bradner. "Click Jahas: Conformationally Restricted Ferrocene-Based Histone Deacetylase Inhibitors."
MedChemComm 3, no. 1 (2012): 61. DOI: 10.1039/C1MD00203A

van Westen, G. J., O. O. van den Hoven, R. van der Pijl, T. Mulder-Krieger, H. de Vries, J. K. Wegner, A. P. Ijzerman, H.
W. van Vlijmen, and A. Bender. "Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of
Rat and Human Bioactivity Data." J Med Chem 55, no. 16 (2012): 7010-20. DOI: 10.1021/jm3003069 

Wang, F., J. A. Good, O. Rath, H. Y. Kaan, O. B. Sutcliffe, S. P. Mackay, and F. Kozielski. "Triphenylbutanamines: Kinesin
Spindle Protein Inhibitors with in Vivo Antitumor Activity." J Med Chem 55, no. 4 (2012): 1511-25. DOI: 10.1021/jm201195m

 

2011

Arshad, A., H. Osman, M. C. Bagley, C. K. Lam, S. Mohamad, and A. S. Zahariluddin. "Synthesis and Antimicrobial Properties
of Some New Thiazolyl Coumarin Derivatives." Eur J Med Chem 46, no. 9 (2011): 3788-94. DOI: 10.1016/j.ejmech.2011.05.044

Bellis, L. J., R. Akhtar, B. Al-Lazikani, F. Atkinson, A. P. Bento, J. Chambers, M. Davies, A. Gaulton, A. Hersey, K.
Ikeda, F. A. Kruger, Y. Light, S. McGlinchey, R. Santos, B. Stauch, and J. P. Overington. "Collation and Data-Mining of
Literature Bioactivity Data for Drug Discovery." Biochem Soc Trans 39, no. 5 (2011): 1365-70. DOI: 10.1042/BST0391365

Deutsch, G. B., E. M. Zielonka, D. Coutandin, T. A. Weber, B. Schafer, J. Hannewald, L. M. Luh, F. G. Durst, M. Ibrahim,
J. Hoffmann, F. H. Niesen, A. Senturk, H. Kunkel, B. Brutschy, E. Schleiff, S. Knapp, A. Acker-Palmer, M. Grez, F. McKeon,
and V. Dotsch. "DNA Damage in Oocytes Induces a Switch of the Quality Control Factor Tap63alpha from Dimer to Tetramer."
Cell 144, no. 4 (2011): 566-76. DOI: 10.1016/j.cell.2011.01.013 

J. Spencer, J. Amin, T.D. Heightman, G. Packham, R.M. Paranal, J.E. Bradner, G. Tizzard and S.J. Coles. "Synthesis and Biological Evaluation of Jahas: Ferrocene-Based Class I Histone Deacetylase Inhibitors." ACS Med Chem Lett 2, no. 5 (2011): 358-362. link 

L. Hopkins, Andrew, G. Richard Bickerton, Ian M. Carruthers, Stephen K. Boyer, Harvey Rubin, and John P. Overington.
"Rapid Analysis of Pharmacology for Infectious Diseases." Current Topics in Medicinal Chemistry 11, no. 10 (2011): 1292-
1300. DOI: 10.2174/156802611795429130 

Miduturu, C. V., X. Deng, N. Kwiatkowski, W. Yang, L. Brault, P. Filippakopoulos, E. Chung, Q. Yang, J. Schwaller, S.
Knapp, R. W. King, J. D. Lee, S. Herrgard, P. Zarrinkar, and N. S. Gray. "High-Throughput Kinase Profiling: A More
Efficient Approach toward the Discovery of New Kinase Inhibitors." Chem Biol 18, no. 7 (2011): 868-79. DOI: 10.1016/j.chembiol.2011.05.010 

Peeters, M. C., G. J. van Westen, Q. Li, and I. Jzerman AP. "Importance of the Extracellular Loops in G Protein-Coupled
Receptors for Ligand Recognition and Receptor Activation." Trends Pharmacol Sci 32, no. 1 (2011): 35-42.
DOI: 10.1016/j.tips.2010.10.001 

Spencer, J., R. P. Rathnam, A. L. Harvey, C. J. Clements, R. L. Clark, M. P. Barrett, P. E. Wong, L. Male, S. J. Coles,
and S. P. Mackay. "Synthesis and Biological Evaluation of 1,4-Benzodiazepin-2-Ones with Antitrypanosomal Activity." Bioorg
Med Chem 19, no. 5 (2011): 1802-15. DOI: 10.1016/j.bmc.2011.01.010 

van Westen, G. J., J. K. Wegner, P. Geluykens, L. Kwanten, I. Vereycken, A. Peeters, A. P. Ijzerman, H. W. van Vlijmen,
and A. Bender. "Which Compound to Select in Lead Optimization? Prospectively Validated Proteochemometric Models Guide
Preclinical Development." PLoS One 6, no. 11 (2011): e27518. DOI: 10.1371/journal.pone.0027518 

van Westen, Gerard J. P., Jörg K. Wegner, Adriaan P. Ijzerman, Herman W. T. van Vlijmen, and A. Bender. "Proteochemometric
Modeling as a Tool to Design Selective Compounds and for Extrapolating to Novel Targets." MedChemComm 2, no. 1 (2011): 16.
DOI: 10.1039/C0MD00165A 

 

2010

Clark, R. L., B. F. Johnston, S. P. Mackay, C. J. Breslin, M. N. Robertson, and A. L. Harvey. "The Drug Discovery Portal:
A Resource to Enhance Drug Discovery from Academia." Drug Discov Today 15, no. 15-16 (2010): 679-83. DOI: 10.1016/j.drudis.2010.06.003 

Clark, R. L., B. F. Johnston, S. P. Mackay, C. J. Breslin, M. N. Robertson, O. B. Sutcliffe, M. J. Dufton, and A. L.
Harvey. "The Drug Discovery Portal: A Computational Platform for Identifying Drug Leads from Academia." Curr Pharm Des 16,
no. 15 (2010): 1697-702. DOI: 10.2174/138161210791164018 

Davis, T., M. A. Bachler, F. S. Wyllie, M. C. Bagley, and D. Kipling. "Evaluating the Role of P38 Map Kinase in Growth of
Werner Syndrome Fibroblasts." Ann N Y Acad Sci 1197, (2010): 45-8. DOI: 10.1111/j.1749-6632.2010.05195.x

Harvey, A. L., R. L. Clark, S. P. Mackay, and B. F. Johnston. "Current Strategies for Drug Discovery through Natural
Products." Expert Opin Drug Discov 5, no. 6 (2010): 559-68. DOI: 10.1517/17460441.2010.488263